, Volume 58, Issue 5–6, pp 433–442 | Cite as

Polymorphism, natural selection, and structural modeling of class Ia MHC in the African clawed frog (Xenopus laevis)

Original Paper


In the African clawed frog (Xenopus laevis), two deeply divergent allelic lineages of multiple genes of the class I MHC region have been discovered. For the MHC class I UAA locus, functional differences and the molecular basis for lineages maintenance are unknown. Alleles of linked class I region genes also exhibit strong disequilibrium with specific MHC alleles, but the underlying cause is not clear. We use MHC class Ia sequence data to estimate substitution rates and investigate structural differences between allelic lineages from protein models. Results indicate the operation of natural selection, and differences in the steric properties in the F pocket of the peptide-binding region among lineages. Variability in this pocket likely enables allelic lineages to bind very different sets of peptides and to interact differently with MHC chaperones in the endoplasmic reticulum. These results constitute evidence of the molecular evolutionary basis for 1) the maintenance of allelic lineages, 2) functional differences among lineages, and 3) strong linkage disequilibrium of allelic variants of class I region genes in X. laevis.


Functional divergence MHC Peptide-binding region Allelic lineages F pocket 



Thanks to Martin Flajnik, Neil Gemmell, the DeWoody lab group, and anonymous peer reviewers for suggestions on earlier versions of this manuscript. Funding is provided by the Marsden Fund (Royal Society of New Zealand) and a Ph.D. scholarship from the University of Canterbury.

Supplementary material

251_2006_114_MOESM1_ESM.pdf (31 kb)
Supplement 1 Phylogenetic trees of amino acid sequence from the MHC class Ia of Xenopus laevis. Trees reconstructed under the maximum likelihood criterion using the JTT model of amino acid changes with a gamma distribution of rate variation among sites. The model was selected as the best-fit model using Akaike’s Information Criterion in the program PROTTEST. Numbers indicate bootstrap support for nodes, and nodes with less than 50% bootstrap support are collapsed into unresolved polytomies. These topologies feature a general lack of resolution due to the short length of the sequences and ambiguous phylogenetic signal (PDF 32 kb)
251_2006_114_MOESM2_ESM.pdf (60 kb)
Supplement 2 (PDF 62 kb)


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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  1. 1.School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
  2. 2.Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteUSA

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